Welcome to Omer’s Website

Hi, This site intended as a portal to Omer Gokcumen’s writings and research. Please contact gokcumen at gmail dot com if you have any questions or if you want to use any of the images/text published in this site.

Origins and functional impact of copy number variation in the human genome

In a collaborative effort that I am involved in, the copy number variation among 20 Yoruban and 20 European individuals are mapped and a portion of these are genotyped across world populations.  This data set will be an important source for the months/years to come for study of the genomes.

For the article: Origins and functional impact of copy number variation in the human genome : Article : Nature.

For the press release: Jumping genes, gene loss and genome dark matter

Yerel bariyerler, genetik karışma ve kıtalararası izolasyon

İTÜ Moleküler Biyoloji ve Genetik Kulübü’nün düzenlediği, İTÜ III. Ulusal Moleküler Biyoloji ve Genetik Öğrenci Kongresi’nde uzaktan bir konferans verme fırsatı buldum.  Gerçekten hem artık bu tip uzaktan konferansların olanaklı olduğunu göstermesi açısından çok hoştu, hem de çok zaman geçirdiğim Boğaziçi Bilim Kulübü’ndeki zamanlarımı hatırlattı.

ITU Talk – 2009

View more presentations from gokcumen.

Konuşmam sırasında, çok kabaca genetik çeşitliliğin ne kadar karmaşık yapılar oluşturduğundan ve bu yapıları ancak şimdi, yeni teknolojiler sayesinde görebildiğimizden bahsettim.  İlginizi çekerse kısaltılmış hali ile slaytlarımı bu sayfada bulabilirsiniz.

Genetik Bilgi – Bilim ve Teknik

A popular science article that I co-authored with Timur Gültekin has been recently put online (to my surprise).  Here is the link to the article:

Genetik Bilgi – TÜBİTAK Bilim ve Teknik Aylık Popüler Bilim Dergisi

A highly annotated whole-genome sequence of a Korean individual

I was a part of a large group of people that characterized, in very fine detail, the genome of a Korean individual.  I think this paper will have a significant impact in many technical subtleties relevant to large sequencing projects.   Also, I think some of the population genetics and biomedical insights are remarkable.  Of course, the emerging importance of copy number variants (CNVs) in shaping genomes is another message underlying this paper.  It is also open access, so you can reach it from Nature’s website.

Copy Number Variants (CNVs) in primate species

We have a new paper out ahead of print in an Elsevier Journal called Methods. Here is the PubMed link.

A substantial amount of genomic variation is now known to exist in humans and other primate species. Single nucleotide polymorphisms (SNPs) are thought to represent the vast majority of genomic differences among individuals in a given primate species and comprise about 0.1% of the genomes of two humans. However, recent studies have now shown that structural variation may account for as much as 0.7% of the genomic differences in humans, of which copy number variants (CNVs) are the largest component. CNVs are segments of DNA that can range in size from hundreds of bases to millions of base pairs in length and have different number of copies between individuals. Recent technological advancements in array technologies led to genome-wide identification of CNVs and consequently revealed thousands of variable loci in humans, comprising as much as 12% of the human genome (iafrate1). CNVs in humans have already been associated with susceptibility to certain complex diseases, dietary adaptation, and several neurological conditions. In addition, recent studies have shown that CNVs can be successfully implemented in population genetics research, providing important insights into human genetic variation. Nevertheless, the important role of CNVs in primate evolution and genetic diversity is still largely unknown. This chapter aims to outline the strengths and weaknesses of current comparative genomic hybridization array technologies that have been employed to detect CNV variation and the applications of these techniques to primate genetic research.

Genetic Anthropology at Fine Scales

Dr. Krishna Veeramah from UCLA and I got a Wenner Gren Foundation grant to organize a workshop.  This event, entitled “Genetic Anthropology at Fine Scales” will host several leading scientists and social scientists to discuss several issues regarding genetic anthropology.  For more information you can visit the website.

Connecting the Genetic Histories of Anatolia: Ethical, Methodological and Theoretical Concerns

Recently, I gave a lecture in  UCLA on the challenges and opportunities in using genetic data to make historical inferences.  The campus of UCLA, by the way, is one of the most beautiful I have ever been.  The lecture was a part of DNA and History seminar series.  It was really nice to see very pronounced efforts to create a multidisciplinary theorotical framework for more nuanced studies of molecular/genetic anthropology.

My talk was constructed on three arguments: (1) The intersection of genetics and history is complex and counter-intuitive in most of the cases, (2) the temporal scale of the sample collection is one of the most important factors in accurately answering the study question; and finally (3) one way to avoid complexities is to conduct very focused, ethnohistorically contextualized studies.  For this last argument, of course I used Anatolian work as an example.

The podcast of this lecture is available.  Please send me an e-mail if you want to watch it, so that I can provide you the necesary information.

Ethnohistorical and genetic survey of four Central Anatolian settlements

My dissertation is recently available through the Penn Library System and ProQuest

ABSTRACT

This study investigates the genetic diversity and ethnohistory of four Central Anatolian settlements from a local perspective to better understand the complex population history of Anatolia. The objectives of this project are to (1) document the biological and cultural diversity in contemporary settlements in the Yuksekyer region, (2) describe the population history of the Yuksekyer settlements within an ethnohistorical context, and (3) contextualize the findings of broader studies, which address major population events, such as the Neolithic expansion and the Turkic invasion, from a local perspective. To accomplish these goals, ethnohistorical fieldwork was conducted using interviews and questionnaires to obtain genealogical information about participants and record the local histories of these settlements, including their cultural and social affinities with each other. During this process, biological samples were also collected from the Yuksekyer inhabitants for genetic analysis. These samples were screened for mtDNA, Y-chromosome, and autosomal polymorphisms, and the resulting data analyzed with statistic and phylogenetic methods to define the biological affinities of Central Anatolian populations, and reconstruct the migration history of the region. The ethnohistorical information obtained through fieldwork facilitated a more thorough historical and cultural understanding of genetic variation in Turkey than has been achieved in previous studies. Furthermore, by working at the local level, it was possible to distinguish patterns of diversity resulting from long-term inhabitation versus those arising from recent immigration into the region. The results of this study revealed that in the village level, the paternal genetic diversity was strongly structured among settlements due to patrilocality. In contrast, maternal genetic diversity is distributed more homogenously. The signatures of Turkic invasion, the Caucasus origins of a particular settlement and recent migrations were all evident in different settlements within Yuksekyer. On the national level, a reassessment of previous genetic studies of Turkish populations indicated that these studies suffer from major sampling bias. Overall, this study emphasizes the value of ethnohistorically contextualized sampling with a multi-allelic genetic analysis to obtain a more complex understanding of the study populations and better delineate the patterns of genetic history in Anatolia.

Marginalia on Marginalism

The  piece “Marginalia on Marginalism in contemporary times” that we wrote we Radu has recently been published in
EXQUISITE CORPSE ANNUAL, NO. 1, 2009