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Uncovering functional variation in humans by genome and transcriptome sequencing

16/09/2013
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Tuuli_chamonix2_croppedDr. Tuuli Lappalainen is a postdoctoral researcher at Stanford University, where she works on functional genetic variation in human populations and specializes in population-scale RNA-sequencing. She kindly agreed to write a guest post on her recent publication in Nature, “Uncovering functional variation in humans by genome and transcriptome sequencing”, which describes work done while she was at the University of Geneva. -DM

In a paper published online today in Nature we describe results of the largest RNA-sequencing study of multiple human populations to date, and provide a comprehensive map of how genetic variation affects the transcriptome. This was achieved by RNA-sequencing of individuals that are part of the 1000 Genomes sample set, thus adding a functional dimension to the most important catalogue of human genomes. In this blog post, I will discuss how our findings shed light on genetic associations to disease.

As genome-wide studies are providing an increasingly comprehensive catalog of genetic variants that predispose to various diseases, we are faced with a huge challenge: what do these variants actually do in the cell? Understanding the biological mechanisms underlying diseases is essential to develop interventions, but traditional molecular biology follow-up is not really feasible for the thousands of discovered GWAS loci. Thus, we need high-throughput approaches for measuring genetic effects at the cellular level, which is an intermediate between the genome and the disease. The cellular trait most amenable for such analysis is the transcriptome, which we can now measure reliably and robustly by RNA-sequencing (as shown by our companion paper in Nature Biotechnology).

In this project, several European institutes of the Geuvadis Consortium sequenced mRNA and small RNA from lymphoblast cell lines from 465 individuals that are in the 1000 Genomes sample set. The idea of gene expression analysis of genetic reference samples is not new (see e.g. papers by Stranger et al., Pickrell et al. and Montgomery et al.), but the bigger scale and better quality enables discovery of exciting new biology.
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Identification of genomic regions shared between distant relatives

13/05/2013
Categories: Guest Posts
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This is a guest post by Graham Coop and Peter Ralph, cross-posted from the Coop Lab website.

We’ve been addressing some of the FAQs on topics arising from our paper on the geography of recent genetic genealogy in Europe (PLOS Biology). We wanted to write one on shared genetic material in personal genomics data but it got a little long, and so we are posting it as its own blog post.

Personal genomics companies that type SNPs genome-wide can identify blocks of shared genetic material between people in their databases, offering the chance to identify distant relatives. Finding a connection to someone else who is an unknown relative is exciting, whether you do this through your family tree or through personal genomics (we’ve both pored over our 23&me results a bunch). However, given the fact that nearly everyone in Europe is related to nearly everyone else over the past 1000 years (see our recent paper and FAQs), and likely everyone in the world is related over the past ~3000 years, how should you interpret that genetic connection?

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No choice for you

28/03/2013
Categories: ELSI
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Guest Co-Author: Dr Anna Middleton is an Ethics Researcher and Registered Genetic Counsellor, based at the Wellcome Trust Sanger Institute, UK.

StethCollage1The American College of Medical Genetics (ACMG) has recently published recommendations for reporting incidental findings (IFs) in clinical exome and genome sequencing. These advocate actively searching for a set of specific IFs unrelated to the condition under study. For example, a two year old child may have her (and her parents’) exome sequenced to explore a diagnosis for intellectual disability and at the same time will be tested for a series of cancer and cardiac genetic variants. The ACMG feel it is unethical not to look for a series of incidental conditions while the genome is being interrogated, conditions that the patient or their family may be able to take steps to prevent. This flies in the face of multiple International guidelines that advise against testing children for adult onset conditions. The ACMG justify this as “a fiduciary duty to prevent harm by warning patients and their families”. They conclude that “this principle supersedes concerns about autonomy”, i.e. the duty of the clinician to perform opportunistic screening outweighs the patients right not to know about other genetic conditions and their right to be able to make autonomous decisions about testing.

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Learning more from your 23andMe results with Imputation

08/03/2013
Categories: DIY and Guest Posts
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PeterAndEliana This is a guest post by Peter Cheng and Eliana Hechter from the University of California, Berkeley.

Suppose that you’ve had your DNA genotyped by 23andMe or some other DTC genetic testing company. Then an article shows up in your morning newspaper or journal (like this one) and suddenly there’s an additional variant you want to know about. You check your raw genotypes file to see if the variant is present on the chip, but it isn’t! So what next? [Note: the most recent 23andMe chip does include this variant, although older versions of their chip do not.]

Genotype imputation is a process used for predicting, or “imputing”, genotypes that are not assayed by a genotyping chip. The process compares the genotyped data from a chip (e.g. your 23andMe results) with a reference panel of genomes (supplied by big genome projects like the 1000 Genomes or HapMap projects) in order to make predictions about variants that aren’t on the chip. If you want a technical review of imputation (and the program IMPUTE in particular), we recommend Marchini & Howie’s 2010 Nature Reviews Genetics article. However, the following figure provides an intuitive understanding of the process.

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Response to “Exaggerations and errors in the promotion of genetic ancestry testing”

03/01/2013
Categories: Guest Posts
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Following the Genomes Unzipped post entitled “Exaggerations and errors in the promotion of genetic ancestry testing”, we received a request to reply from Jim Wilson. Jim Wilson is the chief scientist of BritainsDNA. He is not the one who gave the BBC interview that prompted the Genomes Unzipped post but he is a key contributor to the science behind BritainsDNA. We are keen to tell both sides of this story and this post is an opportunity for BritainsDNA to state their arguments and motivation. -VP

I saw Vincent Plagnol’s post here on Genomes Unzipped about the promotion of genetic ancestry testing and felt compelled to respond. While I did not give the interview that was the subject of the post, I am the chief scientist at BritainsDNA and I feel that the post was biased in presenting only one side of the story and thus misrepresenting the situation. Perhaps I can offer another perspective for readers.

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Guest Post: Jimmy Lin on community-funded rare disease genomics

25/07/2012
Categories: Guest Posts
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Jimmy Cheng-Ho Lin, MD, PhD, MHS is the Founder/President of Rare Genomics Institute, helping patients with rare diseases design, source, and fund personalized genomics projects. He is also on the faculty in the Pathology and Genetics Departments at the Washington University in St. Louis, as part of the Genomics and Pathology Services. Prior to this, he completed his training with Bert Vogelstein and Victor Veculescu at Johns Hopkins and Mark Gerstein at Yale, and led the computational analysis of some of the first exome sequencing projects in any disease, including breast, colorectal, glioblastoma, and pancreatic cancers.

At Rare Genomics Institute (RGI), we have a dream: that one day any parent or community can help access and fund the latest technology for their child with any disease. While nonprofits and foundations exist for many diseases, the vast majority of the 7,000 rare diseases do not have the scientific and philanthropic infrastructure to help. Many parents fight heroically on behalf of their children, and some of them have even become the driving force for research. At RGI, we are inspired by such parents and feel that if we can help provide the right tools and partnerships, extraordinary things can be achieved.

We start by helping parents connect with the right researchers and clinicians. Then, we provide mechanisms for them to fundraise. Finally, we try to guide them through the science that hopefully result in a better life for their child or for future children. Throughout the whole process, we try to educate, support, and walk alongside families undergoing this long journey.
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UK Users’ and Genetics Clinicians’ experiences of direct-to-consumer genetic testing (DTCGT)

08/06/2012
Categories: ELSI
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This is a guest post by Teresa Finlay. Teresa is a PhD student at Cesagen, Cardiff University, studying with Adam Hedgecoe and Michael Arribas-Ayllon. A background in cancer nursing and a degree in human biology informed Teresa’s interest in the public’s use of direct-to-consumer genetic testing to ‘self-screen’ for disease risk. She recently secured funding from the ESRC to research users’ and genetics clinicians’ experiences of DTCGT in the UK. If you are a UK resident who has used a DTC genetic test, or a clinician whose patients have used these tests, then you too can get involved in the research.

Direct-to-consumer genetic testing (DTCGT) has been freely available on the Internet for more than five years, despite concerns from the professional community. Companies marketing these tests (such as 23andMe and deCODEme) claim they are empowering people to make healthy lifestyle choices, and frequently draw on the principle of autonomy as a central argument. This position is confirmed elsewhere by those who view genomic knowledge as an individual right, including many of the bloggers at Genomes Unzipped. Other scientists and clinicians express skepticism about the clinical validity and utility of DTCGT, and raise concerns about the potential for anxiety and inappropriate testing. These debates highlight the importance of research into the motivations and actions of DTCGC customers, but research to date remains very limited, and has mostly been performed on customers in North America. The UK, with its large state-run National Health Service and relative lack of private health insurance and providers, is likely to face unique challenges and situations as DTCGT becomes more common. The paucity of research on UK customers indicates the need for a detailed UK study examining users’ and clinicians’ perspectives in order to establish the long-term implications of DTCGT. This post outlines what is currently known about DTCGT, fills some gaps in the UK context and outlines a research project involving users and clinicians in the UK.

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Guest post: Accurate identification of RNA editing sites from high-throughput sequencing data

16/04/2012
Categories: Journal Club
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[By Gokul Ramaswami and Robert Piskol. Gokul Ramaswami is a graduate student and Robert Piskol is a postdoctoral fellow in the Department of Genetics at Stanford University. Both study RNA editing with Jin Billy Li.]

Thank you to Genomes Unzipped for giving us the opportunity to write about our paper published in Nature Methods [1]. Our goal was to develop a method to identify RNA editing sites using matched DNA and RNA sequencing of the same sample. Looking at the problem initially, it seems straightforward enough to generate a list of variants using the RNA sequencing data and then filter out any variants that also appear in the DNA sequencing. In reality, one must pay close attention to the technical details in order to discern true RNA editing sites from false positives. In this post, we will highlight a couple of key strategies we employed to accurately identify editing sites.
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Guest post by Ben Neale: Evaluating the impact of de novo coding mutation in autism

04/04/2012
Categories: Journal Club
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[Dr. Neale is currently an Assistant in Genetics in the Analytic and Translational Genetics Unit at Massachusetts General Hospital and Harvard Medical School and an affiliate of the Broad Institute of Harvard and MIT. Dr. Neale’s research centers on statistical genetics and how to apply those methods to complex traits, with a particular focus on childhood psychiatric illness such as autism and ADHD.]

Today, in Nature, three letters (1, 2, 3) were published on the role of de novo coding mutations in the development of autism. I am lead author on one of these manuscripts, working in collaboration with the ARRA Autism Consortium. In this post, I’ll describe the main findings of our work as they relate to autism and how we approached the interpretation of de novo mutations. In essence, de novo point mutation is likely relevant to autism in ~10% of cases, but a single de novo event is not likely to be sufficient to cause autism. Underscoring this is that fewer than half of the cases had an obviously functional point mutation in the exome. However, three genes, SCN2A, KATNAL2 and CHD8 have emerged as likely candidates for contributing to autism pathogenesis.

De novo is Latin for “from the beginning,” and when describing genetic variation or mutation means that the variant has spontaneously arisen and was not inherited from either parent. In autism, de novo copy number variants are among the earliest clearly identified genetic risk factors (see Sanders et al. and Pinto et al. for reviews). Given that these events are novel, natural selection has not acted on them, except for instances where the point mutation is lethal in early life. With next generation sequencing (NGS), we now have the opportunity to identify these events directly.

In this study we explored the impact of de novo mutations on autism by performing targeted sequencing of the protein-coding regions of the genome (known collectively as the exome, and comprising just 1.5% of the genome as a whole) in 175 mother-father-child trios in which the child was diagnosed as autistic. Having sequence from all three members of each family allowed us to find mutations that had arisen spontaneously in a patient’s genome, rather than being inherited from their parents.

We have made a pre-formatted version of our manuscript available here. In this post I just wanted to highlight some of the key lessons emerging from our study.
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Guest post: Time to bring human genome sequencing into the clinic

16/02/2012
Categories: Guest Posts
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Gholson Lyon is a physician-scientist currently working at the Utah Foundation for Biomedical Research and the Center for Applied Genomics at Children’s Hospital of Philadelphia. He will be starting as an assistant professor in human genetics at Cold Spring Harbor Laboratory next month. I asked him to write this guest post to provide some personal context to his thought-provoking commentary in Nature (subscription required) on returning genetic findings to research subjects. [DM]

Max

Photo of Max, who died aged four months from Ogden syndrome. Posted with permission from his family.

I have just published in Nature a commentary discussing the need to bring exome and genome sequencing into the clinical arena, so that these data are generated with the same rigorous clinical standards as for any other clinical test. This way, we can then easily return at least medically actionable results to research participants. In this day and age of consumer and patient empowerment, I can also see eventually returning all data, including the raw data, to any interested participants, as this can then promote crowd-sourcing for data analysis, with research participants controlling and promoting the relative privacy of and analysis of their own data.

As I described in my commentary, my thinking on this matter was prompted mainly by Max  (see picture) and his family. The obituary for Max can be found here, and that of his cousin, Sutter, here. We described their condition here, and we named this new disease Ogden Syndrome in honor of where the first family lives. I am now trying to think about and discuss the human aspects of and lessons from this story. My thinking has also been influenced somewhat by the late James Neel, who wrote a very thought-provoking book called Physician to the Gene Pool.

To me, it was deeply disconcerting that I could not officially return any results to this family (or to another family in a different project discussed here) even when the papers describing the genetic basis of their disease were published, as this was considered “research” and was not performed in a clinically appropriate (CLIA-certified) manner. This was all the more painful when one of the sisters in the Ogden family became pregnant and asked me what I knew. I cannot predict whether it would have helped or hurt this woman to learn during her pregnancy that she was indeed a carrier of the mutation, with the associated 50% risk of her baby boy having the disease. I also do not know if she would have undergone any genetic testing via amniocentesis of the fetus prior to birth (with the associated ~1% risk of miscarriage from the procedure), nor do I know what decisions she might have made prior to the birth even if she had undergone such testing. All in all, it was certainly an ethical and moral dilemma for me not to be able to return the research result to her, given that the results were not obtained in a CLIA-certified manner. It is still an issue, as there are even now financial and systematic barriers for getting all women in the family tested with a CLIA-certified gene test for NAA10 (which was developed over a six month period by ARUP Laboratories). It would have been so much better if we had just done the entire sequencing up front in a CLIA-certified manner.
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