Blog Archives

New analyst position in the Bioinformatics Core

The Sheffield Bioinformatics Core will be launching October 2017. A new analyst position has opened up within the Core. This position is suitable for anyone with experience helping others with statistical or computational methods used in the biomedical sciences. As a member of the bioinformatics core team, you will provide a comprehensive portfolio of infrastructure, data analysis, training and development. This is a unique opportunity for you to participate in world-class research while applying best practice and developing new analytical skills and building on your existing expertise. You will be working directly with researchers primarily in the Faculty of Medicine, Dentistry and Health, on projects ranging from interpretation of disease transcriptomics and genome sequences in humans and model organisms.… Full post
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Geographic Population Structure (GPS) technology uncovers ancient Ashkenaz

The origin of the Yiddish language (spoken at least since the 9th century A.D.), and consequently Yiddish speakers, has been debated for the past several centuries, mainly between linguists. While the Rhineland hypothesis suggests a German origin, the Irano-Turko-Slavic hypothesis, proposed by Paul Wexler, suggests a more complex origin starting with Slavic lands in Khazaria, followed by Ukraine, and finally Germany where the language was relexified, i.e., adopted a German vocabulary, but retained its Slavic grammar, which is why Yiddish was oftentimes called “Bad German.” To evaluate these two hypotheses we applied the Geographic Population Structure (GPS) tool to the genomes of over 360 sole Yiddish and non-Yiddish speaking Ashkenazic Jews.… Full post
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Largest human population sequencing study to date (UK10K project) published in Nature

The findings of the UK10K study, a project to sequence the genomes of nearly 10,000 individuals, mostly from the UK, have been published online in Nature. Lucy Crooks is one of the lead authors. The project performed whole genome sequencing on nearly 4,000 healthy individuals and exome sequencing of over 5,000 people affected with diseases including schizophrenia, obesity and a collection of rare diseases. The study explored the role of low frequency and rare variants in disease risk and provides a reference panel of genetic variation in the UK population to apply in future research.… Full post
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The dysregulated pathway that drives us low and high

Bipolar disorder refers to a chronic condition that consists of mood swings between two different mood poles, the high pole (mania) and the low pole (depression). In the course of their illness, bipolar patients may endure an increase in the frequency and severity of symptoms termed progression. Inflammation is the most potent biological mechanism to explain this progression, however, thus far no specific mechanism was identified. The over activation of immune response, observed in bipolar patients, may be due to the dysregulation of Nf-kb, a key regulator of the immune system. In Elhaik and Zandi 2015, we wrote the first review of NF-kB’s involvement in bipolar disorder.… Full post
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Unraveling the compositional architecture of mammalian genomes

For the past four decades the compositional organization of the mammalian genome posed a formidable challenge to molecular evolutionists attempting to explain it from an evolutionary perspective. We have carried the most detailed analyses to describe mammalian genome composition thus far. We debunked the “isochore theory,” which argues that the genome consists of long stretches of homogeneous DNA, and showed that it actually consists of many short and few long domains. We also found evidence to that invalidate the Euarchontoglire clade, suggesting that primates are not closer to murids more than to Laurasiatheria. Our paper was published in PloS Computational biology.… Full post
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How old is “Adam Y chromosome”?

In early 2014, Mendez and colleague announced the identification of a Y chromosome haplotype (the A00 lineage) that is the most ancient Y chromosome (commonly termed “Adam Y chromosome”). The authors estimated its age at 338,000 years, at odds with all previous estimates in the literature and over a 100,000 years older than the earliest fossils of anatomically modern humans. In a series of three papers, we demonstrated that the age estimate was reached through inadequate statistical and analytical methods, both of which contributed to its inflation. Our analysis indicated that the A00 lineage was derived from all the other lineages 208,000 years ago.… Full post
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A new tool: Geographic Population Structure (GPS) infers biogeographical origin down to home village from your DNA

  In 2014, Elhaik and colleagues published the Geographic Population Structure (GPS) tool in Nature Communications. GPS is the most accurate tool for predicting the geographic origin of world populations up to the past 1000 years. For example, the authors have demonstrated the accuracy of their tool using Oceanian islanders and Sardinian villagers. The concept of GPS rests on a new paradigm that assumes all human genomes are mixtures of different gene pools. You can learn more by watching this video and reading about the ongoing research in Dr. Elhaik’s lab. An FAQ page about GPS is available in Dr.Full post
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