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Tracing Family Trees, And Human History, With Genetics

Participating in the World Science Festival, NYC. Lot’s of fun.

It’s All Relatives: The Science of Your Family Tree

Join us at the World Science Festival! Thursday May 29th, 6pm. Hosted by the New York Historical Society.

We welcome Misha Lipatov as a postdoctoral scholar in the Henn Lab. Misha joins us from Stanford University, where he completed his PhD with Marc Feldman and Dmitri Petrov, working on mathematical models of evolutionary biology.

We welcome Misha Lipatov as a postdoctoral scholar in the Henn Lab. Misha joins us from Stanford University, where he completed his PhD with Marc Feldman and Dmitri Petrov, working on mathematical models of evolutionary biology.

New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

More insight into the population history of Europeans, using ancient DNA, by the Bustamante Lab (and colleagues).

Exome capture from saliva produces high quality genomic and metagenomic data
Provisional pdf now online at BMC Genomics (2014) 15:262
Jeffrey M Kidd, Thomas J Sharpton, Dean Bobo, Paul J Norman, Alicia R Martin, Meredith L Carpenter, Martin Sikora, Christopher R Gignoux, Neda Nemat-Gorgani, Alexandra Adams,Moraima Guadalupe, Xiaosen Guo, Qiang Feng, Yingrui Li, Xiao Liu, Peter Parham, Eileen G Hoal, Marcus W Feldman, Katherine S Pollard, Jeffrey D Wall, Carlos D Bustamante and Brenna M Henn


Background

Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research.

Results

We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data.

Conclusions

DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.

Exome capture from saliva produces high quality genomic and metagenomic data

Provisional pdf now online at BMC Genomics (2014) 15:262

Jeffrey M Kidd, Thomas J Sharpton, Dean Bobo, Paul J Norman, Alicia R Martin, Meredith L Carpenter, Martin Sikora, Christopher R Gignoux, Neda Nemat-Gorgani, Alexandra Adams,Moraima Guadalupe, Xiaosen Guo, Qiang Feng, Yingrui Li, Xiao Liu, Peter Parham, Eileen G Hoal, Marcus W Feldman, Katherine S Pollard, Jeffrey D Wall, Carlos D Bustamante and Brenna M Henn

Background

Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research.

Results

We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data.

Conclusions

DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.

Laura Botigue received a prestigious 2014 Beatriu de Pinós Programme Postdoctoral Fellowship from the government of Catalonia to continue her work on human population genetics for the next two years in the Henn Lab. Congratulations Laura!

Laura Botigue received a prestigious 2014 Beatriu de Pinós Programme Postdoctoral Fellowship from the government of Catalonia to continue her work on human population genetics for the next two years in the Henn Lab. Congratulations Laura!

Discover Magazine Top 100 List

Recalibrating the human Y chromosome (Poznik et al. 2013, Science) makes Discover Magazine’s list of the top 100 stories in 2013.

EMBO conference on Human Evolutionary Genetics, April 1-4, 2014.  Consider submitting an Abstract!

EMBO conference on Human Evolutionary Genetics, April 1-4, 2014.  Consider submitting an Abstract!

Field season for 2013 is finally over. Flying over northern Namibia, evidence of the extreme drought (top) and talking with Himba families (bottom).

Collection of links to news articles about our recent Y-chromosome Science paper that do a good job of providing context for the science: LA Times, PopSci, Christian Science Monitor, among others.   

Our paper “Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females" is now online at Science. 
The Y chromosome and the mitochondrial genome have been used to estimate when the common patrilineal and matrilineal ancestors of humans lived. We sequenced the genomes of 69 males from nine populations, including two in which we find basal branches of the Y-chromosome tree. We identify ancient phylogenetic structure within African haplogroups and resolve a long-standing ambiguity deep within the tree. Applying equivalent methodologies to the Y chromosome and the mitochondrial genome, we estimate the time to the most recent common ancestor (TMRCA) of the Y chromosome to be 120 to 156 thousand years and the mitochondrial genome TMRCA to be 99 to 148 thousand years. Our findings suggest that, contrary to previous claims, male lineages do not coalesce significantly more recently than female lineages.

Our paper “Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females" is now online at Science. 

The Y chromosome and the mitochondrial genome have been used to estimate when the common patrilineal and matrilineal ancestors of humans lived. We sequenced the genomes of 69 males from nine populations, including two in which we find basal branches of the Y-chromosome tree. We identify ancient phylogenetic structure within African haplogroups and resolve a long-standing ambiguity deep within the tree. Applying equivalent methodologies to the Y chromosome and the mitochondrial genome, we estimate the time to the most recent common ancestor (TMRCA) of the Y chromosome to be 120 to 156 thousand years and the mitochondrial genome TMRCA to be 99 to 148 thousand years. Our findings suggest that, contrary to previous claims, male lineages do not coalesce significantly more recently than female lineages.

Brenna and Chris teaching population and statistical genetics at the H3ABioNet “Train the Trainers” Bioinformatics Workshop in Nairobi, Kenya. Workshop students are members of a NIH/Wellcome Trust H3Africa initiative to build and support a bioinformatics network across many African institutions for human genomic research. 

Brenna and Chris teaching population and statistical genetics at the H3ABioNet “Train the Trainers” Bioinformatics Workshop in Nairobi, Kenya. Workshop students are members of a NIH/Wellcome Trust H3Africa initiative to build and support a bioinformatics network across many African institutions for human genomic research. 

Image from Skorecki and Behar’s detailed commentary ‘North Africans Traveling North' in this week's PNAS. 

Image from Skorecki and Behar’s detailed commentary ‘North Africans Traveling North' in this week's PNAS. 

Gene flow from North Africa contribute to differential genetic diversity in southern Europe is published in the current issue of PNAS.  In This Issue.  Congratulations Laura!

Gene flow from North Africa contribute to differential genetic diversity in southern Europe is published in the current issue of PNAS.  In This Issue.  Congratulations Laura!