Itsik Pe'er - Research

The Pe'er lab is actively recruiting talented individuals for undergraduate credit projects, programming positions, graduate and postdoctoral studies. Contact me for details.

Overview: The Pe'er Lab Studies, Develops and Applies Novel Computational Methods in Human Genetics

How is it best to measure, describe and quantify differences between individual DNA sequences? How does sequence variation affect biological processes? How can we use it to understand and influence human disease? All these questions pose complex analytical challenges, with direct impact on medical research.

Human genetics is as ancient as human history. It's computational foundations are intertwined with the most fundamental developments in statistics. Such quantifications reveal the tremendous degree to which medical traits are heritable, and motivate a large research community to investigate the interconnections between gene variants (genotypes) and observed traits (phenotypes). The third millennium finds genetics more flourishing than ever with high throughput technologies generating large scale data sets, yet with more need than ever of computational innovation and methods to process these data into meaningful biomedical insights. The upcoming era, of complete genotype information available to each individual on the planet therefore holds the potential of great discoveries, and poses the challenges of powerful and rigorous analyses of these data.


Genetics of Common Variants: Genomewide Association Studies

Whole genome arrays of Single Nucleotide Polymorphisms (SNPs) and Copy Number Variants (CNVs) have been designed to represent common variation in the human genome, aiming to associate such variation with health-related traits. We are involved in the analysis of such Genomewide Association Study (GWAS) data across multiple phenotypes:

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Genetics of Rare Variants: Identity by Descent between Purported Unrelated Individuals

The co-inheritance of long haplotypes in recent generations is key to the analysis of rare variants carried on the background of these segments that are Identical By Descent (IBD). We have developed a linear-time algorithm to scan a large population for IBD segments without the quadratic exhaustive search of all pairs of individuals. This enables genomewide analysis of thousands of samples, and paves the way to multiple avenues of research. Specifically, we have been using IBD in unrelateds to inform phasing, deletion detection, population structure, and fine-mapping of associated variants. Read more


High Throughput Sequencing for Comprehensively Cataloging Variants

While most of the current genetic data is based on SNP markers, DNA sequencing has been increasing in throughput and cost-effectiveness out-pacing Moore's law. We have been developing and applying computational methods to tackle this torrent of sequence data. Specifically, we have refined models of genomic coverage in worm resequencing data, observing they fit a Gamma distribution, rather than a Poisson model. We further developed a novel method for sequencing of DNA from pools of individuals. The method designs overlapping pools, so that an individual carrier of a discovered variant can be traced through the intersection of such pools. Error Correcting Codes make such pool designs robust to experimental and statistical error. Read more


Somatic vs. Germline Genetic Variation and Its Effect on Cancer

Cancer is a genetic illness of cells. Somatic lineages suffer loss and gain of parts of the genome. As somatic copy number changes occur randomly, but may be sometimes selected for in tumorgenesis, we are investigating the allele specificity of this selection, i.e., the connections between an individual's germline genotype and the observed copy number changes in the tumor's somatic genotypes.
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A word about updates and backward compatibility: Ideally, this page would be always up to date. However, in practice it is overhauled on occasion, and then left as it is. During the current update (Oct. 2008), I found it refreshing, humbling and overall educating to reflect on my research interests as I wrote them down in August 2006.


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