The current buzz about about GWAS and longevity and GWAS in general has stirred up many longstanding inconvenient issues that arise when trying to interpret the results of very large, expensive and worthwhile genetic studies. Its seems that Mother Nature does not give up her secrets without a fight.
One of the most common “inconvenient issues” is the fact that so many of the SNPs that come out of these studies are located far away from protein-encoding exons. This ubiquitous observation is almost always followed with, “well, maybe its in linkage disequilibrium with a more functional SNP” or something along these lines – wherein the authors get an automatic pass. OK by me.
Another “inconvenient issue” is the fact that many of these SNPs are of minimal effect and don’t exactly add up or interact to account for the expected heritability. This problem of “missing heritability” is a big one (see some new insights in the latest issue of Nature Genetics) leading many to suspect that the effects of genes are dependent on complex interactions with each other and the environment.
A recent paper, “A map of open chromatin in human pancreatic islets” [doi:10.1038/ng.530] by Gaulton and colleagues caught my eye because it seems to shed light on both of these particular inconvenient issues. The authors find that the diabetes risk variant rs7903146 in the TCF7L2 gene is both located in an intron and subject to epigenetic regulation (our sedentary, high-fat, high-stress lives can potentially interact with the genome by causing epigenetic change).
It appears that the T-allele of the intronic rs7903146 is correlated with a more open, transcription-prone form of DNA/chromatin than is the C-allele. The authors confirmed this using both chromatin mapping and gene expression assays on pancreatic islet cells harvested from non-diabetic donors and islet cell-lines. The results suggest that the risk-conferring T-allele of this intronic SNP may be driving expression (gain-of-function) of the TCF7L2 gene. What types of environmental stimuli might also impact the opening and closing of chromatin at this location?
This type of interplay of environment, genome and epigenome is probably rampant in the area of brain and behavior – so perhaps the study of diabetes will provide some clues to the many GWAS SNPs that are far away from exons. More on the genetics of epigenetics here.
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Posted in Chromosome structural variants, Intronic or repetitive sequences, Uncategorized, tagged Add new tag, Biology, bipolardisorder, Copy number variation, Depression, DNA, Gene, Genetic testing, Genetic variation, Genetics, Genome-wide association study, Mental disorder, Mental health, Single-nucleotide polymorphism, Twin, Twin study on April 5, 2010|
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Twin studies have long suggested that genetic variation is a part of healthy and disordered mental life. The problem however – some 10 years now since the full genome sequence era began – has been finding the actual genes that account for this heritability.
It sounds simple on paper – just collect lots of folks with disorder X and look at their genomes in reference to a demographically matched healthy control population. Voila! whatever is different is a candidate for genetic risk. Apparently, not so.
The missing heritability problem that clouds the birth of the personal genomes era refers to the baffling inability to find enough common genetic variants that can account for the genetic risk of an illness or disorder.
There are any number of reasons for this … (i) even as any given MZ and DZ twin pair shares genetic variants that predispose them toward the similar brains and mental states, it may be the case that different MZ and DZ pairs have different types of rare genetic variation thus diluting out any similar patterns of variation when large pools of cases and controls are compared … (ii) also, the way that the environment interacts with common risk-promoting genetic variation may be quite different from person to person – making it hard to find variation that is similarly risk-promoting in large pools of cases and controls … and many others I’m sure.
One research group recently asked whether the type of common genetic variation(SNP vs. CNV) might inform the search for the missing heritability. The authors of the recent paper, “Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls” [doi:10.1038/nature08979] looked at an alternative to the usual SNP markers – so called common copy number variants (CNVs) – and asked if these markers might provide a stronger accounting for genetic risk. While a number of previous papers in the mental health field have indeed shown associations with CNVs, this massive study (some 3,432 CNV probes in 2000 or so cases and 3000 controls) did not reveal an association with bipolar disorder. Furthermore, the team reports that common CNV variants are already in fairly strong linkage disequilibrium with common SNPs and so perhaps may not have reached any farther into the abyss of rare genetic variation than previous GWAS studies.
Disappointing perhaps, but a big step forward nonetheless! What will the personal genomes era look like if we all have different forms of rare genetic variation?
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Posted in Chromosome structural variants, Intronic or repetitive sequences, tagged autism, Autism spectrum, Cognition, Genetic testing, Mental disorder, Mental health, Neural development, Neurodevelopmental, schizophrenia on December 7, 2009|
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The recent paper, “Comparative genomics of autism and schizophrenia” by Bernard Crespi and colleagues provides a very exciting take on how genetic data can be mined to understand cognitive development and mental illness. Looking at genetic association data for autism and schizophrenia, the authors point out that 4 loci are associated with both schizophrenia and autism – however, with a particular twist. In the case of 1q21.1 and 22q11.21 it seems that genetic deletions are associated with schizophrenia while duplications at this locus are associated with autism. At 16p11.2 and 22q13.3 it seems that duplications are associated with schizophrenia and deletions are associated with autism. Thus both loci contain genes that regulate brain development such that too much (duplication) or too little (deletion) of these genes can cause brain development to go awry. The authors point to genes involved in cellular and synaptic growth for which loss-of-function in growth inhibition genes (which would cause overgrowth) have been associated with autism while loss-of-function in growth promoting genes (which would cause undergrowth) have been associated with schizophrenia. Certainly there is much evidence for overproduction of synapses in the autism-spectrum disorders and loss of synapses in schizophrenia. Crespi et al., [doi:10.1073/pnas.0906080106]
Other research covered (here, here) demonstrates the importance of the proper balance of excitatory and inhibitory signalling during cortical development.
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Posted in Intronic or repetitive sequences, tagged Biology, DNA, DNA sequence, evolution, Gene, Genome, RNA, Stem cell, Transposon on August 8, 2009|
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For more than a decade, we’ve known that at least 95% of the human genome is junk – or junque – if you’re offended by the thought that “you” emerged from a single cell whose genome is mostly a vast pile of crap – or crappe – if you insist. Hmmm, what is this crap? It turns out to be a lot of random repeating sequences and a massive collection of evolutionary artifacts left over from the evolution of earlier genomes – mainly bits of retroviruses who once inserted themselves irreversibly into our ancestors’ genomes. One subset of this type of – can we upgrade it from crappe to “relic” now? – is something we’ve labelled “autonomously mobile DNA sequences” or more specifically, “long interspersed nuclear elements (LINEs or L1s)”. This class of DNA relic comprises more than 15% of the human genome (that’s about 3-5x more than the relevant genomic sequence from which you emerge) and retains the ability to pick itself up out of the genome – via an RNA intermediate – and insert itself into new places in the genome. This has been observed to happen in the germ line of humans and a few L1 insertions are even responsible for genetic forms of humn disease (for example in the factor VIII gene giving rise to haemophilia). The mechanism of transposition – or “jumping” as these elements are sometimes called “jumping genes” – involves the assembly of a certain type of transcriptional, transport and reverse-transcription (RNA back to DNA) apparatus that is known to be available in stem cells, but hardly ever in somatic cells.
Except, it would seem, for the brain – which as we’ve covered here before – keeps its precious neurons and glia functioning under separate rules. Let’s face it, if a liver cell dies, you just replace it without notice, but if neurons die, so do your childhood memories. So its not too surprising, perhaps, that brain cells have special ‘stem-cell-like’ rules for keeping themselves youthful. This seems to be borne out again in a paper entitled, “L1 retrotransposition in human neural progenitor cells” by Coufal et al., [doi:10.1038/nature08248]. Here the team shows that L1 elements are able to transpose themselves in neural stem cells and that there are more L1 elements (about 80 copies more per cell) in the hippocampus than in liver or heart cells. So apparently, the hippocampus, which does seem to contain a niche of stem cells, permits the transposition or “jumping” of L1 elements in a way that the liver and heart do not. Sounds like a fun place to be a gene!
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