Archive for the ‘DNA’ tag
deCODE Genetics Discovers Three Variants in the Sequence of the Human Genome that Affect the Risk of Thyroid Cancer
Scientists at deCODE Genetics and academic collaborators from Iceland, the USA, The Netherlands and Spain today report the discovery of variants in the human genome that associate with levels of thyroid stimulating hormone and risk of thyroid cancer. The paper ‘Discovery of common variants associated with low TSH levels and thyroid cancer risk‘ is published today in the online edition of Nature Genetics.
Using data obtained by applying both Illumina whole-genome sequencing technology and Illumina SNP chip technology, deCODE’s scientists performed a genome wide association study on levels of thyroid stimulating hormone (TSH) in 27,758 Icelanders. 22 SNPs with genomewide significance were discovered, of which one, rs965513 had previously been shown to associate with thyroid cancer. The remaining 21 SNPs were genotyped in 561 Icelandic thyroid cancer cases and 40,013 controls. Variants suggestively associated with thyroid cancer were then genotyped in an additional 595 non-Icelandic cases and 2,603 controls.
After combining the results, three separate variants on chromosomes 2q35, 8p12 and 14q13.3 were shown to associate with risk of thyroid cancer, conferring an added risk of 30 – 100%, compared to the general population. These variants were also found to associate with low levels of TSH, a key regulator in the biology and endocrinology of the thyroid gland.
“This study underscores the important role that the genetics of diversity in normal physiologic function can play in understanding the risk of disease. To date, the at-risk alleles of all the variants that confer risk of thyroid cancer associate with decreased serum levels of TSH, suggesting that the primary disorder in non-medullary thyroid cancer is an endocrine one, characterized by decreased concentration of TSH,” said Kari Stefansson, deCODE’s CEO and senior author of the study.
Thyroid Cancer is a malignant thyroid neoplasm, which can be treated with radioactive iodine or surgical resection of the thyroid gland. The contribution of genetics to the risk of thyroid cancer is greater than to any other cancer. Thyroid cancer is classified into four main histology groups: papillary (PTC), follicular (FTC), medullary (MTC), and undifferentiated or anaplastic thyroid carcinomas. The great majority of malignant thyroid tumours are nonmedullary, either PTC (80–85%) or FTC (10–15%).
deCODE Announces Agreement with Pfizer to Search for Variants in the Human Genome that Confer Risk of Systemic Lupus Erythematosis
deCODE genetics today announced that it has entered into a research collaboration with Pfizer Inc., the objective of which is to discover sequence variants associated with specific clinical phenotypes related to Systemic Lupus Erythematosis by utilizing deCODE‘s expertise in gene discovery.
deCODE’s discovery capabilities combine its extensive population and genetic resources, including DNA samples and medical data, complete genealogical information, next generation sequencing technology, and deCODE’s proprietary bioinformatics and statistical capabilities. Over the next 18 months, deCODE and Pfizer will work together to analyse the genomes of patients to search for sequence variants that would be useful for understanding drug targets and discovering novel drug targets, that may ultimately lead to tools for patient stratification and companion diagnostics.
“This agreement is a part of deCODE’s ongoing strategy to unleash the value of human genetics,” said Dr. Kari Stefansson, founder and CEO of deCODE, “our research platform allows us to understand the genetic basis of disease and modifiers of clinical phenotypes in actual patient populations; by doing so, we can rapidly move from targets to patient stratification and from there to companion diagnostics.”
The research collaboration will utilize the expertise and capabilities of both deCODE and Pfizer: deCODE’s comprehensive population genetics resources and analytical expertise and Pfizer’s dedication to the application of genomic analysis to the discovery and development of drugs.
deCODE genetics, Together with Academic Collaborators and Illumina, Discovers Genetic Risk Factor for Skin, Prostate and Brain Cancers
Scientists at deCODE Genetics and academic collaborators from Iceland, The Netherlands, Spain, Denmark, Germany, Sweden, the USA, the UK and Romania today report the discovery of a variant in the sequence of the human genome associated with risk of developing basal cell carcinoma of the skin (BCC), as well as prostate cancer and glioma, the most serious form of brain cancer. The study was done in collaboration with Illumina, Inc., and is published today in the online edition of Nature Genetics.
Using Illumina sequencing technology, deCODE scientists determined the sequences of the entire genomes of 457 Icelanders, and identified 16 million single nucleotide polymorphisms (SNPs). Through a combination of SNP genotyping and computational techniques utilizing the extensive Icelandic genealogy, they were able to propagate those 16 million variants into over 40,000 Icelanders for use in this study.
The researchers discovered a single letter variant located in TP53, a gene known to play a central role in tumor biology and for accumulating so called somatic mutations, during the development of cancer in patients. Until now, however, individuals who are born with defective copies of the gene (germline variants) have been found extremely rarely, only in families with cancer predisposition syndromes, Li Fraumeni syndrome (LFS) and Li-Fraumeni-like syndrome (LFL). The variant found in the present study is an unusual type of mutation that appears to affect the way the gene’s messenger RNA is processed; the messenger RNA in patients with the mutant TP53 gene appears to lack proper termination and polyadenylation.
This is the first evidence of a germline variant in TP53 associated with cancer predisposition beyond LFS and LFL. While the mutations causing LFS and LFL syndromes are very rare (occuring 1:5,000 to 1:20,000 births), the variant described in this paper occurs in ~ 1 in 25 individuals in Iceland, and at comparable frequencies in US and UK populations.
“This mutation is one of a growing number of deCODE discoveries of relatively low frequency sequence variants with large effect,” said Kari Stefansson, deCODE’s CEO and senior author of the study. “The discovery of such variants is made possible through the breadth and quality of the data that the Icelandic population provides.”
Dr. Stefansson emphasized, “We will, together with our collaborators, including Illumina, extend ourselves to turn this discovery into benefit for patients and those at risk of cancer.”
BCC is the most common cancer in people of European ancestry. Sun exposure is the primary risk factor for BCC, but genetic predisposition also plays a substantial role. Until now, no mechanistic causal connection between cancers as diverse as BCC, prostate cancer, glioma, and colorectal adenoma was known.
The paper, “A Germline Variant in the TP53 Polyadenylation Signal Confers Cancer Susceptibility” is published online in Nature Genetics at www.nature.com/ng and will appear in an upcoming print edition of the journal.
We have just made some updates to the deCODEme ancestry service. Now you have more power and flexibility when you compare your genome with that of friends or individuals from different populations around the world.
Your genome can be viewed as a mosaic or tapestry made up of fragments of chromosomes from your ancestors. Fragments of chromosomes inherited from very recent ancestors, say grandparents, are expected to be large – typically tens of millions of nucleotides in size. As ancestors become more ancient, then the size of the chromosome fragments inherited from them become smaller – down to a few thousand or hundred nucleotides for ancestors born thousands of years ago.
Our new and improved genome comparison tool enables to you compare your genome with another individual in order to determine which chromosome fragments you share and to see how much of your genome is shared. The fascinating thing about this analysis is that each shared fragment represents a common ancestor. The number of shared fragments and their size reflects the number of common ancestors and how far back in time they are found. In other words, you can see how closely you are related.
deCODEme for “Curious George” – A catalog of published results from the National Human Genome Research Institute
Through your deCODEme account (or the demo account if you are not yet a deCODEme customer) you can access a catalog of published Genome-Wide Association Studies (GWAS) that has been compiled by the National Human Genome Research Institute (NHGRI).
This feature allows you to gain a quick overview of where research on common traits has been showing associations with single nucleotide genetic variations (SNPs). Users can easily select a disease or trait from a list and a feature track with the corresponding SNPs from the catalog will show up in our Genome Browser.
Many of the associations in the GWAS catalog compiled in August 2009 are included in our Health Watch feature. There are also numerous other associations that our scientists have not included, as they do not fulfill the criteria we set for inclusion in our Health Watch.
The GWAS catalog is presented (see here) simply as it appears on the NHGRI web site and has not been reviewed by deCODE’s scientists. The catalog is provided primarily for educational purposes – for the curious George who wants to look at genome-wide association study results in the context of other information that we provide in our Genome Browser.
Ovarian cancer is the eighth most common cancer in women. Based on ovarian cancer statistics in the U.S., it is expected that 1.4% of women born today will be diagnosed with cancer of the ovary at some point during their lifetime. This represents the lifetime risk of ovarian cancer and means that 1 out of every 71 women will be diagnosed with this disease during their lifetime. deCODEme Complete Scan now includes risk calculation for Ovarian Cancer.
Stories from our foremothers: deCODE publishes an unparalleled genetic snapshot of Iceland 1000 years ago
In a paper published today scientists at deCODE genetics present the results of the largest study of ancient DNA from a single population ever undertaken. Analyzing mitochondrial DNA, which is passed from mother to offspring, from 68 skeletal remains from approximately 1000 years ago, the study provides the most detailed look to date at how a contemporary population differs from that of its ancestors. The results confirm previous deCODE work that used genetics to test the history of Iceland as recorded in the sagas.
These studies demonstrated that the country seems indeed to have been settled by men from Scandinavia – the vikings – but that the majority of the original female inhabitants were from the coastal regions of Scotland and Ireland, areas that regularly suffered raids by vikings in the years around the settlement of Iceland 1100 years ago.
Perhaps the most remarkable finding of the study published today is that the gene pool of contemporary Icelanders appears to have evolved rapidly over the intervening thousand years. As a result, the original female settlers are genetically more closely related to the present day populations of Scotland, Ireland and Scandinavia, as well as those of northwestern Europe and even southwestern Europe, than they are to present day Icelanders. This is an important demonstration of a phenomenon known as ‘genetic drift.’ In essence, in any population certain individuals will have more offspring and, by chance and in this case over the course of 35 generations, many more descendants than others. And as a result, particularly in a small population, the genetic variety of the original population can decrease and change over time. In this study only mitochondrial DNA was studied, but the same phenomenon applies to the Y chromosome, which is passed from fathers to sons, and to any other part of the genome. The paper, ‘Sequences from first settlers reveal rapid evolution in Icelandic mtDNA pool,’ is published today in the open-access journal PLOS Genetics.
“This study is a major contribution to the use of ancient DNA studies in tracing the history not just of single populations, but of our species and how we spread from Africa to every corner of the globe. It is the first such study to be large enough to permit meaningful statistical methods to be applied to ancient DNA. We very much hope this will aid and encourage others to follow with large studies in other parts of the world. In this field, as in the genetics of common diseases, we are pleased and proud to be able to put the knowledge we gain in Iceland to work for the benefit of people everywhere,” said Kari Stefansson, CEO of deCODE.
The number of companies offering genetic tests to the public is large and growing. But there are vast and very real differences in the quality, purpose and price of testing services out there. So how do you tell the difference between them? And how do you decide which to use?
Knowing what you want
First and foremost, you need to think about what sort of information you hope to gain from your genome and how accurate you want the results to be. Are you taking the test only for fun, perhaps hoping to talk about your results on Facebook? Read the rest of this entry »
deCODE and Radboud University discover common variants in the human genome conferring risk of bladder cancer
Urinary bladder cancer is something many people have never heard of. But it is the sixth most common form of cancer in the United States, and its environmental risk factors include exposure to toxic chemicals, including some used in industrial processing as well as cigarette smoke. Genetic factors also play a role and may help to elucidate how bladder cancer starts and develops.
Today, deCODE’s cancer group and colleagues at Radboud University in the Netherlands report the discovery of two single letter variants (commonly referred to as SNPs) in the human genome that confer increased risk of bladder cancer. Both are common, and 20 percent of people of European descent carry two copies of the highest impact SNP, located on chromosome 8q24. That puts them at about 50 percent higher likelihood of developing bladder cancer than people who do not carry the variant.
Our genomes are all remarkably similar. And so it is the differences that are most interesting and important, and that make us who we are.
The same can be said of genetic testing services. We at deCODE were not at all surprised that Mr. Fleming found that he got some varying results from the three genome scans that he tried. Indeed we would be surprised (and more than a little dismayed) if he hadn’t. Analyzing the genome – accurately detecting which genetic markers individuals have at specific points in the genome, and correlating these variations with risk of a range of common diseases – has been our bread and butter for well over a decade. Read the rest of this entry »